Alex Dyer claims Livingston refused to delay their Premiership clash with Kilmarnock on Saturday.
The Ayrshire club's first-team squad was advised to self-isolate following six positive Covid-19 tests, with their match against Motherwell earlier in the month postponed.
The Rugby Park outfit then had to forfeit last week's Betfred Cup Group E opener against Falkirk after Dyer refused to play a team of youth players.
The Killie boss has five senior outfield players and a goalkeeper available for the home Betfred Cup tie against Dunfermline on Tuesday night, with the rest of his missing players making their way back for the weekend and the trip to Livingston.
Dyer said: "I asked if we could have the game put back two or three days. That was a no.
"So we sent an email to the league and they said Livi didn't want to respond again so we have to play the game.
"It's not great because we're all here to help one another.
"We're going through a situation in the whole of the country, not just in football.
"It's a pandemic. So I am asking for a little bit of fairness so my players can come back and make sure they're right for the game.
"But that's not the case, we have to play the game long as I've got 13 fit players.
"It is disappointing because it would be fair for someone to give us a little bit more time, because it could happen to any football club.
"It could happen to anyone in society so why wouldn't it happen to any football club? And then, like I said, people should help one another.
"But it is not to be, we move on and we have to play the game and if I have enough fit bodies then I will do that, not a problem."
Dyer is also disgruntled about the investigation launched by the SPFL following the direction to the Killie squad to self-isolate.
He said: "I don't think there should be an investigation.
"We've done the right things and we've followed all the guidelines.
"We try and take steps where we can restrict it a little bit, but it's there and it will get worse.
"I'm clear that we do the right things at this football club.
"If they find something I don't know about then I don't know.
"We got good backroom staff, the doctor has been excellent, we have been given the right protocols to follow and to do the right things. There's nothing more we can do."
